Nextflow workflow report

Workflow execution completed unsuccessfully!

The exit status of the task that caused the workflow execution to fail was: 1.

The full error message was:

Error executing process > 'prepGWAS_shah'

Caused by:
  Process `prepGWAS_shah` terminated with an error exit status (1)

Command executed:

  module load gcc/11.4.0 openmpi/4.1.4 R/4.3.1
  
  # Run analysis script
  Rscript /standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/scripts/standardize_GWAS_eQTL_for_coloc_new.R \
      --gwas ShahS_31919418_HeartFailure.gz \
      --prefix shah20_gwas_HF \
      --liftover TRUE

Command exit status:
  1

Command output:
  [1] "Finished standardizing columns"
  [1] "Processing LiftOver!"

Command error:
  
  The following object is masked from ‘package:utils’:
  
      findMatches
  
  The following objects are masked from ‘package:base’:
  
      expand.grid, I, unname
  
  Loading required package: IRanges
  
  Attaching package: ‘IRanges’
  
  The following object is masked from ‘package:lubridate’:
  
      %within%
  
  The following objects are masked from ‘package:dplyr’:
  
      collapse, desc, slice
  
  The following object is masked from ‘package:purrr’:
  
      reduce
  
  The following object is masked from ‘package:data.table’:
  
      shift
  
  Loading required package: GenomeInfoDb
  Discarding unchained sequences: 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 5, 6, 7, 8, 9, 1, 2, 3, 4
  Loading required package: BSgenome
  Loading required package: Biostrings
  Loading required package: XVector
  
  Attaching package: ‘XVector’
  
  The following object is masked from ‘package:purrr’:
  
      compact
  
  
  Attaching package: ‘Biostrings’
  
  The following object is masked from ‘package:base’:
  
      strsplit
  
  Error: object 'gwasTest' not found
  Execution halted

Work dir:
  /sfs/ceph/standard/vol185/cphg_Manichaikul/users/csm6hg/nextflow_dna/work/14/54e4fd2773cdbd346aa6036630fa63

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`